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- PDB-1pax: THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1pax
TitleTHE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH 3,4-DIHYDRO-5-METHYL-ISOQUINOLINONE
ComponentsPOLY(ADP-RIBOSE) POLYMERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / NAD(+) ADP-RIBOSYLTRANSFERASE
Function / homology
Function and homology information


NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / NAD+-protein-serine ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / ATP generation from poly-ADP-D-ribose / replication fork reversal / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation ...NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / NAD+-protein-serine ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / ATP generation from poly-ADP-D-ribose / replication fork reversal / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / nuclear replication fork / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of double-strand break repair via homologous recombination / NAD+-protein poly-ADP-ribosyltransferase activity / nucleosome binding / negative regulation of innate immune response / nucleotidyltransferase activity / NAD binding / double-strand break repair / site of double-strand break / damaged DNA binding / innate immune response / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / cytosol
Similarity search - Function
Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / : / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 ...Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / : / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3,4-DIHYDRO-5-METHYL-ISOQUINOLINONE / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsRuf, A. / Schulz, G.E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Structure of the catalytic fragment of poly(ADP-ribose) polymerase from chicken.
Authors: Ruf, A. / Mennissier de Murcia, J. / de Murcia, G. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and X-Ray Crystallographic Analysis of Recombinant Chicken Poly (Adp-Ribose) Polymerase Catalytic Domain Produced in Sf9 Insect Cells
Authors: Jung, S. / Miranda, E.A. / Menissier De Murcia, J. / Niedergang, C. / Delarue, M. / Schulz, G.E. / De Murcia, G.M.
History
DepositionMay 6, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLY(ADP-RIBOSE) POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5772
Polymers40,4151
Non-polymers1611
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.200, 64.500, 96.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein POLY(ADP-RIBOSE) POLYMERASE / PARP-CF / POLY(ADP-RIBOSE) TRANSFERASE / POLY (ADP-RIBOSE) SYNTHETASE


Mass: 40415.352 Da / Num. of mol.: 1 / Fragment: CATALYTIC FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell line: SF9 / Organelle: NUCLEUS / Plasmid: PVLPE / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P26446, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-DHQ / 3,4-DIHYDRO-5-METHYL-ISOQUINOLINONE


Mass: 161.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 47 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Jung, S., (1994) J.Mol.Biol., 244, 114.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.05 %(w/v)beta-OG1drop
23.75 mg/mlprotein1drop
32.5 mMAp4A1drop
48.5 %(w/v)PEG40001drop
54 %(v/v)2-propanol1drop
635 mMTris-HCl1drop
717 %(w/v)PEG40001reservoir
88 %(v/v)2-propanol1reservoir
970 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Mar 29, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→11.9 Å / Num. obs: 14941 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.295 / % possible all: 94.4

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
X-PLOR3.851phasing
RefinementResolution: 2.4→11.9 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.244 -10 %
Rwork0.169 --
obs0.169 14941 99.3 %
Displacement parametersBiso mean: 35.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→11.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 12 83 2858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.3
X-RAY DIFFRACTIONx_mcangle_it3.7
X-RAY DIFFRACTIONx_scbond_it4.4
X-RAY DIFFRACTIONx_scangle_it6.8

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